1
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Yi HB, Lee S, Seo K, Kim H, Kim M, Lee HS. Cellular and Biophysical Applications of Genetic Code Expansion. Chem Rev 2024; 124:7465-7530. [PMID: 38753805 DOI: 10.1021/acs.chemrev.4c00112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2024]
Abstract
Despite their diverse functions, proteins are inherently constructed from a limited set of building blocks. These compositional constraints pose significant challenges to protein research and its practical applications. Strategically manipulating the cellular protein synthesis system to incorporate novel building blocks has emerged as a critical approach for overcoming these constraints in protein research and application. In the past two decades, the field of genetic code expansion (GCE) has achieved significant advancements, enabling the integration of numerous novel functionalities into proteins across a variety of organisms. This technological evolution has paved the way for the extensive application of genetic code expansion across multiple domains, including protein imaging, the introduction of probes for protein research, analysis of protein-protein interactions, spatiotemporal control of protein function, exploration of proteome changes induced by external stimuli, and the synthesis of proteins endowed with novel functions. In this comprehensive Review, we aim to provide an overview of cellular and biophysical applications that have employed GCE technology over the past two decades.
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Affiliation(s)
- Han Bin Yi
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Seungeun Lee
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Kyungdeok Seo
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Hyeongjo Kim
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Minah Kim
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Hyun Soo Lee
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
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2
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Gordon SE, Evans EGB, Otto SC, Tessmer MH, Shaffer KD, Gordon MT, Petersson EJ, Stoll S, Zagotta WN. Long-distance tmFRET using bipyridyl- and phenanthroline-based ligands. Biophys J 2024:S0006-3495(24)00092-4. [PMID: 38350449 DOI: 10.1016/j.bpj.2024.01.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 12/27/2023] [Accepted: 01/29/2024] [Indexed: 02/15/2024] Open
Abstract
With the great progress on determining protein structures over the last decade comes a renewed appreciation that structures must be combined with dynamics and energetics to understand function. Fluorescence spectroscopy, specifically Förster resonance energy transfer (FRET), provides a great window into dynamics and energetics due to its application at physiological temperatures and ability to measure dynamics on the ångström scale. We have recently advanced transition metal FRET (tmFRET) to study allosteric regulation of maltose binding protein and have reported measurements of maltose-dependent distance changes with an accuracy of ∼1.5 Å. When paired with the noncanonical amino acid Acd as a donor, our previous tmFRET acceptors were useful over a working distance of 10 to 20 Å. Here, we use cysteine-reactive bipyridyl and phenanthroline compounds as chelators for Fe2+ and Ru2+ to produce novel tmFRET acceptors to expand the working distance to as long as 50 Å, while preserving our ability to resolve even small maltose-dependent changes in distance. We compare our measured FRET efficiencies to predictions based on models using rotameric ensembles of the donors and acceptors to demonstrate that steady-state measurements of tmFRET with our new probes have unprecedented ability to measure conformational rearrangements under physiological conditions.
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Affiliation(s)
- Sharona E Gordon
- Department of Physiology and Biophysics, University of Washington, Seattle, Washington.
| | - Eric G B Evans
- Department of Physiology and Biophysics, University of Washington, Seattle, Washington; Department of Chemistry, University of Washington, Seattle, Washington
| | - Shauna C Otto
- Department of Physiology and Biophysics, University of Washington, Seattle, Washington
| | - Maxx H Tessmer
- Department of Chemistry, University of Washington, Seattle, Washington
| | - Kyle D Shaffer
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Moshe T Gordon
- Department of Physiology and Biophysics, University of Washington, Seattle, Washington
| | - E James Petersson
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Stefan Stoll
- Department of Chemistry, University of Washington, Seattle, Washington
| | - William N Zagotta
- Department of Physiology and Biophysics, University of Washington, Seattle, Washington.
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3
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Zagotta WN, Evans EGB, Eggan P, Tessmer MH, Shaffer KD, Petersson EJ, Stoll S, Gordon SE. Measuring conformational equilibria in allosteric proteins with time-resolved tmFRET. Biophys J 2024:S0006-3495(24)00091-2. [PMID: 38303511 DOI: 10.1016/j.bpj.2024.01.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 01/28/2024] [Accepted: 01/29/2024] [Indexed: 02/03/2024] Open
Abstract
Proteins are the workhorses of biology, orchestrating a myriad of cellular functions through intricate conformational changes. Protein allostery, the phenomenon where binding of ligands or environmental changes induce conformational rearrangements in the protein, is fundamental to these processes. We have previously shown that transition metal Förster resonance energy transfer (tmFRET) can be used to interrogate the conformational rearrangements associated with protein allostery and have recently introduced novel FRET acceptors utilizing metal-bipyridyl derivatives to measure long (>20 Å) intramolecular distances in proteins. Here, we combine our tmFRET system with fluorescence lifetime measurements to measure the distances, conformational heterogeneity, and energetics of maltose-binding protein, a model allosteric protein. Time-resolved tmFRET captures near-instantaneous snapshots of distance distributions, offering insights into protein dynamics. We show that time-resolved tmFRET can accurately determine distance distributions and conformational heterogeneity of proteins. Our results demonstrate the sensitivity of time-resolved tmFRET in detecting subtle conformational or energetic changes in protein conformations, which are crucial for understanding allostery. In addition, we extend the use of metal-bipyridyl compounds, showing that Cu(phen)2+ can serve as a spin label for pulse dipolar electron paramagnetic resonance (EPR) spectroscopy, a method that also reveals distance distributions and conformational heterogeneity. The EPR studies both establish Cu(phen)2+ as a useful spin label for pulse dipolar EPR and validate our time-resolved tmFRET measurements. Our approach offers a versatile tool for deciphering conformational landscapes and understanding the regulatory mechanisms governing biological processes.
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Affiliation(s)
- William N Zagotta
- Department of Physiology and Biophysics, University of Washington, Seattle, Washington.
| | - Eric G B Evans
- Department of Physiology and Biophysics, University of Washington, Seattle, Washington; Department of Chemistry, University of Washington, Seattle, Washington
| | - Pierce Eggan
- Department of Physiology and Biophysics, University of Washington, Seattle, Washington
| | - Maxx H Tessmer
- Department of Chemistry, University of Washington, Seattle, Washington
| | - Kyle D Shaffer
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania
| | - E James Petersson
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Stefan Stoll
- Department of Chemistry, University of Washington, Seattle, Washington
| | - Sharona E Gordon
- Department of Physiology and Biophysics, University of Washington, Seattle, Washington.
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4
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Kyrychenko A, Ladokhin AS. Fluorescent Probes and Quenchers in Studies of Protein Folding and Protein-Lipid Interactions. CHEM REC 2024; 24:e202300232. [PMID: 37695081 PMCID: PMC11113672 DOI: 10.1002/tcr.202300232] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 08/20/2023] [Indexed: 09/12/2023]
Abstract
Fluorescence spectroscopy provides numerous methodological tools for structural and functional studies of biological macromolecules and their complexes. All fluorescence-based approaches require either existence of an intrinsic probe or an introduction of an extrinsic one. Moreover, studies of complex systems often require an additional introduction of a specific quencher molecule acting in combination with a fluorophore to provide structural or thermodynamic information. Here, we review the fundamentals and summarize the latest progress in applications of different classes of fluorescent probes and their specific quenchers, aimed at studies of protein folding and protein-membrane interactions. Specifically, we discuss various environment-sensitive dyes, FRET probes, probes for short-distance measurements, and several probe-quencher pairs for studies of membrane penetration of proteins and peptides. The goals of this review are: (a) to familiarize the readership with the general concept that complex biological systems often require both a probe and a quencher to decipher mechanistic details of functioning and (b) to provide example of the immediate applications of the described methods.
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Affiliation(s)
- Alexander Kyrychenko
- Institute of Chemistry and School of Chemistry, V. N. Karazin Kharkiv National University, 4 Svobody sq., Kharkiv, 61022, Ukraine
| | - Alexey S Ladokhin
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, KS, 66160, United States
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5
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Zagotta WN, Evans EGB, Eggan P, Tessmer MH, Shaffer KD, Petersson EJ, Stoll S, Gordon SE. Measuring conformational equilibria in allosteric proteins with time-resolved tmFRET. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.09.561594. [PMID: 37873384 PMCID: PMC10592786 DOI: 10.1101/2023.10.09.561594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Proteins are the workhorses of biology, orchestrating a myriad of cellular functions through intricate conformational changes. Protein allostery, the phenomenon where binding of ligands or environmental changes induce conformational rearrangements in the protein, is fundamental to these processes. We have previously shown that transition metal Förster resonance energy transfer (tmFRET) can be used to interrogate the conformational rearrangements associated with protein allostery and have recently introduced novel FRET acceptors utilizing metal-bipyridyl derivatives to measure long (>20 Å) intramolecular distances in proteins. Here, we combine our tmFRET system with fluorescence lifetime measurements to measure the distances, conformational heterogeneity, and energetics of maltose binding protein (MBP), a model allosteric protein. Time-resolved tmFRET captures near-instantaneous snapshots of distance distributions, offering insights into protein dynamics. We show that time-resolved tmFRET can accurately determine distance distributions and conformational heterogeneity of proteins. Our results demonstrate the sensitivity of time-resolved tmFRET in detecting subtle conformational or energetic changes in protein conformations, which are crucial for understanding allostery. In addition, we extend the use of metal-bipyridyl compounds, showing Cu(phen)2+ can serve as a spin label for pulse dipolar electron paramagnetic resonance (EPR) spectroscopy, a method which also reveals distance distributions and conformational heterogeneity. The EPR studies both establish Cu(phen)2+ as a useful spin label for pulse dipolar EPR and validate our time-resolved tmFRET measurements. Our approach offers a versatile tool for deciphering conformational landscapes and understanding the regulatory mechanisms governing biological processes.
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Affiliation(s)
- William N. Zagotta
- Department of Physiology and Biophysics, University of Washington, Seattle, Washington 98195
| | - Eric G. B. Evans
- Department of Physiology and Biophysics, University of Washington, Seattle, Washington 98195
- Department of Chemistry, University of Washington, Seattle, Washington 98195
| | - Pierce Eggan
- Department of Physiology and Biophysics, University of Washington, Seattle, Washington 98195
| | - Maxx H. Tessmer
- Department of Chemistry, University of Washington, Seattle, Washington 98195
| | - Kyle D. Shaffer
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104
| | - E. James Petersson
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104
| | - Stefan Stoll
- Department of Chemistry, University of Washington, Seattle, Washington 98195
| | - Sharona E. Gordon
- Department of Physiology and Biophysics, University of Washington, Seattle, Washington 98195
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6
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Gordon SE, Evans EGB, Otto SC, Tessmer MH, Shaffer KD, Gordon MT, Petersson EJ, Stoll S, Zagotta WN. Long-distance tmFRET using bipyridyl- and phenanthroline-based ligands. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.09.561591. [PMID: 37873407 PMCID: PMC10592757 DOI: 10.1101/2023.10.09.561591] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
With the great progress on determining protein structures over the last decade comes a renewed appreciation that structures must be combined with dynamics and energetics to understand function. Fluorescence spectroscopy, specifically Förster resonance energy transfer (FRET), provides a great window into dynamics and energetics due to its application at physiological temperatures and ability to measure dynamics on the ångström scale. We have recently advanced transition metal FRET (tmFRET) to study allosteric regulation of maltose binding protein and have reported measurements of maltose-dependent distance changes with an accuracy of ~1.5 Å. When paired with the noncanonical amino acid Acd as a donor, our previous tmFRET acceptors were useful over a working distance of 10 Å to 20 Å. Here, we use cysteine-reactive bipyridyl and phenanthroline compounds as chelators for Fe2+ and Ru2+ to produce novel tmFRET acceptors to expand the working distance to as long as 50 Å, while preserving our ability to resolve even small maltose-dependent changes in distance. We compare our measured FRET efficiencies to predictions based on models using rotameric ensembles of the donors and acceptors to demonstrate that steady-state measurements of tmFRET with our new probes have unprecedented ability to measure conformational rearrangements under physiological conditions.
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Affiliation(s)
- Sharona E. Gordon
- Department of Physiology and Biophysics, University of Washington, Seattle, Washington 98195
| | - Eric G. B. Evans
- Department of Physiology and Biophysics, University of Washington, Seattle, Washington 98195
- Department of Chemistry, University of Washington, Seattle, Washington 98195
| | - Shauna C. Otto
- Department of Physiology and Biophysics, University of Washington, Seattle, Washington 98195
| | - Maxx H. Tessmer
- Department of Chemistry, University of Washington, Seattle, Washington 98195
| | - Kyle D. Shaffer
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104
| | - Moshe T. Gordon
- Department of Physiology and Biophysics, University of Washington, Seattle, Washington 98195
| | - E. James Petersson
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104
| | - Stefan Stoll
- Department of Chemistry, University of Washington, Seattle, Washington 98195
| | - William N. Zagotta
- Department of Physiology and Biophysics, University of Washington, Seattle, Washington 98195
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7
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Hu Z, Zheng X, Yang J. Conformational trajectory of allosteric gating of the human cone photoreceptor cyclic nucleotide-gated channel. Nat Commun 2023; 14:4284. [PMID: 37463923 DOI: 10.1038/s41467-023-39971-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 07/05/2023] [Indexed: 07/20/2023] Open
Abstract
Cyclic nucleotide-gated (CNG) channels transduce chemical signals into electrical signals in sensory receptors and neurons. They are activated by cGMP or cAMP, which bind to the cyclic nucleotide-binding domain (CNBD) to open a gate located 50-60 Å away in the central cavity. Structures of closed and open vertebrate CNG channels have been solved, but the conformational landscape of this allosteric gating remains to be elucidated and enriched. Here, we report structures of the cGMP-activated human cone photoreceptor CNGA3/CNGB3 channel in closed, intermediate, pre-open and open states in detergent or lipid nanodisc, all with fully bound cGMP. The pre-open and open states are obtained only in the lipid nanodisc, suggesting a critical role of lipids in tuning the energetic landscape of CNGA3/CNGB3 activation. The different states exhibit subunit-unique, incremental and distinct conformational rearrangements that originate in the CNBD, propagate through the gating ring to the transmembrane domain, and gradually open the S6 cavity gate. Our work illustrates a spatial conformational-change wave of allosteric gating of a vertebrate CNG channel by its natural ligand and provides an expanded framework for studying CNG properties and channelopathy.
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Affiliation(s)
- Zhengshan Hu
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA
| | - Xiangdong Zheng
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA
| | - Jian Yang
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA.
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8
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Jana S, Evans EGB, Jang HS, Zhang S, Zhang H, Rajca A, Gordon SE, Zagotta WN, Stoll S, Mehl RA. Ultrafast Bioorthogonal Spin-Labeling and Distance Measurements in Mammalian Cells Using Small, Genetically Encoded Tetrazine Amino Acids. J Am Chem Soc 2023; 145:14608-14620. [PMID: 37364003 PMCID: PMC10440187 DOI: 10.1021/jacs.3c00967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
Site-directed spin-labeling (SDSL)─in combination with double electron-electron resonance (DEER) spectroscopy─has emerged as a powerful technique for determining both the structural states and the conformational equilibria of biomacromolecules. DEER combined with in situ SDSL in live cells is challenging since current bioorthogonal labeling approaches are too slow to allow for complete labeling with low concentrations of spin label prior to loss of signal from cellular reduction. Here, we overcome this limitation by genetically encoding a novel family of small, tetrazine-bearing noncanonical amino acids (Tet-v4.0) at multiple sites in proteins expressed in Escherichia coli and in human HEK293T cells. We achieved specific and quantitative spin-labeling of Tet-v4.0-containing proteins by developing a series of strained trans-cyclooctene (sTCO)-functionalized nitroxides─including a gem-diethyl-substituted nitroxide with enhanced stability in cells─with rate constants that can exceed 106 M-1 s-1. The remarkable speed of the Tet-v4.0/sTCO reaction allowed efficient spin-labeling of proteins in live cells within minutes, requiring only sub-micromolar concentrations of sTCO-nitroxide. DEER recorded from intact cells revealed distance distributions in good agreement with those measured from proteins purified and labeled in vitro. Furthermore, DEER was able to resolve the maltose-dependent conformational change of Tet-v4.0-incorporated and spin-labeled MBP in vitro and support assignment of the conformational state of an MBP mutant within HEK293T cells. We anticipate the exceptional reaction rates of this system, combined with the relatively short and rigid side chains of the resulting spin labels, will enable structure/function studies of proteins directly in cells, without any requirements for protein purification.
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Affiliation(s)
- Subhashis Jana
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, United States
| | - Eric G B Evans
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
- Department of Physiology & Biophysics, University of Washington, Seattle, Washington 98195, United States
| | - Hyo Sang Jang
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, United States
| | - Shuyang Zhang
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588-0304, United States
| | - Hui Zhang
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588-0304, United States
| | - Andrzej Rajca
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588-0304, United States
| | - Sharona E Gordon
- Department of Physiology & Biophysics, University of Washington, Seattle, Washington 98195, United States
| | - William N Zagotta
- Department of Physiology & Biophysics, University of Washington, Seattle, Washington 98195, United States
| | - Stefan Stoll
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Ryan A Mehl
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, United States
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9
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Cory MB, Jones CM, Shaffer KD, Venkatesh Y, Giannakoulias S, Perez RM, Lougee MG, Hummingbird E, Pagar VV, Hurley CM, Li A, Mach RH, Kohli RM, Petersson EJ. FRETing about the details: Case studies in the use of a genetically encoded fluorescent amino acid for distance-dependent energy transfer. Protein Sci 2023; 32:e4633. [PMID: 36974585 PMCID: PMC10108435 DOI: 10.1002/pro.4633] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Revised: 03/22/2023] [Accepted: 03/24/2023] [Indexed: 03/29/2023]
Abstract
Förster resonance energy transfer (FRET) is a valuable method for monitoring protein conformation and biomolecular interactions. Intrinsically fluorescent amino acids that can be genetically encoded, such as acridonylalanine (Acd), are particularly useful for FRET studies. However, quantitative interpretation of FRET data to derive distance information requires careful use of controls and consideration of photophysical effects. Here we present two case studies illustrating how Acd can be used in FRET experiments to study small molecule induced conformational changes and multicomponent biomolecular complexes.
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Affiliation(s)
- Michael B. Cory
- Graduate Group in Biochemistry and BiophysicsPerelman School of Medicine, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
| | - Chloe M. Jones
- Graduate Group in Biochemistry and BiophysicsPerelman School of Medicine, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
| | - Kyle D. Shaffer
- Department of ChemistrySchool of Arts and Sciences, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
| | - Yarra Venkatesh
- Department of ChemistrySchool of Arts and Sciences, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
| | - Sam Giannakoulias
- Department of ChemistrySchool of Arts and Sciences, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
| | - Ryann M. Perez
- Department of ChemistrySchool of Arts and Sciences, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
| | - Marshall G. Lougee
- Department of ChemistrySchool of Arts and Sciences, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
| | - Eshe Hummingbird
- Department of ChemistrySchool of Arts and Sciences, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
| | - Vinayak V. Pagar
- Department of ChemistrySchool of Arts and Sciences, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
| | - Christina M. Hurley
- Graduate Group in Biochemistry and BiophysicsPerelman School of Medicine, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
| | - Allen Li
- Department of ChemistrySchool of Arts and Sciences, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
| | - Robert H. Mach
- Department of RadiologyPerelman School of Medicine, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
| | - Rahul M. Kohli
- Department of Biochemistry and BiophysicsPerelman School of Medicine, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
- Department of MedicinePerelman School of Medicine, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
| | - E. James Petersson
- Department of ChemistrySchool of Arts and Sciences, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
- Department of Biochemistry and BiophysicsPerelman School of Medicine, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
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10
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Jana S, Evans EGB, Jang HS, Zhang S, Zhang H, Rajca A, Gordon SE, Zagotta WN, Stoll S, Mehl RA. Ultra-Fast Bioorthogonal Spin-Labeling and Distance Measurements in Mammalian Cells Using Small, Genetically Encoded Tetrazine Amino Acids. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.26.525763. [PMID: 36747808 PMCID: PMC9901033 DOI: 10.1101/2023.01.26.525763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Studying protein structures and dynamics directly in the cellular environments in which they function is essential to fully understand the molecular mechanisms underlying cellular processes. Site-directed spin-labeling (SDSL)-in combination with double electron-electron resonance (DEER) spectroscopy-has emerged as a powerful technique for determining both the structural states and the conformational equilibria of biomacromolecules. In-cell DEER spectroscopy on proteins in mammalian cells has thus far not been possible due to the notable challenges of spin-labeling in live cells. In-cell SDSL requires exquisite biorthogonality, high labeling reaction rates and low background signal from unreacted residual spin label. While the bioorthogonal reaction must be highly specific and proceed under physiological conditions, many spin labels display time-dependent instability in the reducing cellular environment. Additionally, high concentrations of spin label can be toxic. Thus, an exceptionally fast bioorthogonal reaction is required that can allow for complete labeling with low concentrations of spin-label prior to loss of signal. Here we utilized genetic code expansion to site-specifically encode a novel family of small, tetrazine-bearing non-canonical amino acids (Tet-v4.0) at multiple sites in green fluorescent protein (GFP) and maltose binding protein (MBP) expressed both in E. coli and in human HEK293T cells. We achieved specific and quantitative spin-labeling of Tet-v4.0-containing proteins by developing a series of strained trans -cyclooctene (sTCO)-functionalized nitroxides-including a gem -diethyl-substituted nitroxide with enhanced stability in cells-with rate constants that can exceed 10 6 M -1 s -1 . The remarkable speed of the Tet-v4.0/sTCO reaction allowed efficient spin-labeling of proteins in live HEK293T cells within minutes, requiring only sub-micromolar concentrations of sTCO-nitroxide added directly to the culture medium. DEER recorded from intact cells revealed distance distributions in good agreement with those measured from proteins purified and labeled in vitro . Furthermore, DEER was able to resolve the maltose-dependent conformational change of Tet-v4.0-incorporated and spin-labeled MBP in vitro and successfully discerned the conformational state of MBP within HEK293T cells. We anticipate the exceptional reaction rates of this system, combined with the relatively short and rigid side chains of the resulting spin labels, will enable structure/function studies of proteins directly in cells, without any requirements for protein purification. TOC
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Affiliation(s)
- Subhashis Jana
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, United States
- Equal contributors
| | - Eric G B Evans
- Department of Chemistry, University of Washington, Seattle, WA 98195, United States
- Department of Physiology & Biophysics, University of Washington, Seattle, WA 98195, United States
- Equal contributors
| | - Hyo Sang Jang
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, United States
| | - Shuyang Zhang
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588-0304, United States
| | - Hui Zhang
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588-0304, United States
| | - Andrzej Rajca
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588-0304, United States
| | - Sharona E Gordon
- Department of Physiology & Biophysics, University of Washington, Seattle, WA 98195, United States
| | - William N Zagotta
- Department of Physiology & Biophysics, University of Washington, Seattle, WA 98195, United States
| | - Stefan Stoll
- Department of Chemistry, University of Washington, Seattle, WA 98195, United States
| | - Ryan A Mehl
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, United States
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11
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Durner A, Durner E, Nicke A. Improved ANAP incorporation and VCF analysis reveal details of P2X7 current facilitation and a limited conformational interplay between ATP binding and the intracellular ballast domain. eLife 2023; 12:82479. [PMID: 36598131 PMCID: PMC9859053 DOI: 10.7554/elife.82479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 01/03/2023] [Indexed: 01/05/2023] Open
Abstract
The large intracellular C-terminus of the pro-inflammatory P2X7 ion channel receptor (P2X7R) is associated with diverse P2X7R-specific functions. Cryo-EM structures of the closed and ATP-bound open full-length P2X7R recently identified a membrane-associated anchoring domain, an open-state stabilizing "cap" domain, and a globular "ballast domain" containing GTP/GDP and dinuclear Zn2+-binding sites with unknown functions. To investigate protein dynamics during channel activation, we improved incorporation of the environment-sensitive fluorescent unnatural amino acid L-3-(6-acetylnaphthalen-2-ylamino)-2-aminopropanoic acid (ANAP) into Xenopus laevis oocyte-expressed P2X7Rs and performed voltage clamp fluorometry. While we confirmed predicted conformational changes within the extracellular and the transmembrane domains, only 3 out of 41 mutants containing ANAP in the C-terminal domain resulted in ATP-induced fluorescence changes. We conclude that the ballast domain functions rather independently from the extracellular ATP binding domain and might require activation by additional ligands and/or protein interactions. Novel tools to study these are presented.
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Affiliation(s)
- Anna Durner
- Walther Straub Institute of Pharmacology and Toxicology, Faculty of Medicine, LMU MunichMunichGermany
| | - Ellis Durner
- Lehrstuhl für Angewandte Physik and Center for Nanoscience, LMU MunichMunichGermany
| | - Annette Nicke
- Walther Straub Institute of Pharmacology and Toxicology, Faculty of Medicine, LMU MunichMunichGermany
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